|
super-focus
|
public |
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
|
2025-04-22 |
|
r-sigtree
|
public |
Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.
|
2025-04-22 |
|
r-phyext2
|
public |
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
|
2025-04-22 |
|
r-pma
|
public |
Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in the following papers: (1) Witten, Tibshirani and Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology 8(1): Article 28.
|
2025-04-22 |
|
r-treesim
|
public |
Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
|
2025-04-22 |
|
r-geiger
|
public |
Methods for fitting macroevolutionary models to phylogenetic trees.
|
2025-04-22 |
|
bax2bam
|
public |
bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format
|
2025-04-22 |
|
genomelake
|
public |
Simple and efficient random access to genomic data for deep learning models.
|
2025-04-22 |
|
r-ncbit
|
public |
making NCBI taxonomic data locally available and searchable as an R object
|
2025-04-22 |
|
r-phytools
|
public |
Phylogenetic tools for comparative biology
|
2025-04-22 |
|
r-msm
|
public |
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. Designed for processes observed at arbitrary times in continuous time (panel data) but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.
|
2025-04-22 |
|
splicemap
|
public |
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy.
|
2025-04-22 |
|
biopet-extractadaptersfastqc
|
public |
ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report.
|
2025-04-22 |
|
flash2
|
public |
Merge paired-end reads from fragments that are shorter than twice the read length
|
2025-04-22 |
|
r-metalonda
|
public |
Identify time intervals of differentially abundant metagenomics features in longitudinal studies.
|
2025-04-22 |
|
r-nodiv
|
public |
An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
|
2025-04-22 |
|
r-annotables
|
public |
Provides tables for converting and annotating Ensembl Gene IDs.
|
2025-04-22 |
|
snpiphy
|
public |
An automated snp phylogeny pipeline
|
2025-04-22 |
|
ctat-mutations
|
public |
Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.
|
2025-04-22 |
|
r-spieceasi
|
public |
Estimate networks from the precision matrix of compositional microbial abundance data.
|
2025-04-22 |
|
r-structssi
|
public |
Performs multiple testing corrections that take specific structure of hypotheses into account.
|
2025-04-22 |
|
r-aptreeshape
|
public |
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) and Maliet et al. (2017).
|
2025-04-22 |
|
goalign
|
public |
goalign is a set of command line tools to manipulate multiple alignments
|
2025-04-22 |
|
gotree
|
public |
gotree is a set of command line tools to manipulate phylogenetic trees
|
2025-04-22 |
|
iclipro
|
public |
iCLIPro is a Python package that can be used to control for systematic misassignments in iCLIP data.
|
2025-04-22 |
